[English] 日本語
Yorodumi
- PDB-3vma: Crystal Structure of the Full-Length Transglycosylase PBP1b from ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3vma
TitleCrystal Structure of the Full-Length Transglycosylase PBP1b from Escherichia coli
ComponentsPenicillin-binding protein 1B
KeywordsTRANSFERASE / HYDROLASE/ANTIBIOTIC / bacterial cell wall synthesis / penicillin-binding protein / antibiotics design / PBP3 / MipA / MltA / FtsN / Membrane / HYDROLASE-ANTIBIOTIC complex
Function / homology
Function and homology information


positive regulation of bipolar cell growth / cell wall repair / peptidoglycan glycosyltransferase / peptidoglycan glycosyltransferase activity / serine-type D-Ala-D-Ala carboxypeptidase / serine-type D-Ala-D-Ala carboxypeptidase activity / penicillin binding / peptidoglycan biosynthetic process / peptidoglycan-based cell wall / outer membrane-bounded periplasmic space ...positive regulation of bipolar cell growth / cell wall repair / peptidoglycan glycosyltransferase / peptidoglycan glycosyltransferase activity / serine-type D-Ala-D-Ala carboxypeptidase / serine-type D-Ala-D-Ala carboxypeptidase activity / penicillin binding / peptidoglycan biosynthetic process / peptidoglycan-based cell wall / outer membrane-bounded periplasmic space / regulation of cell shape / response to antibiotic / proteolysis / membrane / plasma membrane
Similarity search - Function
Penicillin-binding protein 1B / Bifunctional transglycosylase second domain / Transglycosylase PBP1b, N-terminal transmembrane domain / Transmembrane domain of transglycosylase PBP1 at N-terminal / Bifunctional transglycosylase second domain / Penicillin-binding protein 1b fold / Penicillin-binding protein 1b domain / Penicillin binding protein transpeptidase fold / Biosynthetic peptidoglycan transglycosylase-like / Glycosyl transferase, family 51 ...Penicillin-binding protein 1B / Bifunctional transglycosylase second domain / Transglycosylase PBP1b, N-terminal transmembrane domain / Transmembrane domain of transglycosylase PBP1 at N-terminal / Bifunctional transglycosylase second domain / Penicillin-binding protein 1b fold / Penicillin-binding protein 1b domain / Penicillin binding protein transpeptidase fold / Biosynthetic peptidoglycan transglycosylase-like / Glycosyl transferase, family 51 / Penicillin binding protein transglycosylase domain / Transglycosylase / Cytochrome c1, transmembrane anchor, C-terminal / Penicillin-binding protein, transpeptidase / Penicillin binding protein transpeptidase domain / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Beta-lactamase/transpeptidase-like / Lysozyme-like domain superfamily / Up-down Bundle / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
MOENOMYCIN / Penicillin-binding protein 1B
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.161 Å
AuthorsHuang, C.Y. / Sung, M.T. / Lai, Y.T. / Chou, L.Y. / Shih, H.W. / Cheng, W.C. / Wong, C.H. / Ma, C.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2009
Title: Crystal structure of the membrane-bound bifunctional transglycosylase PBP1b from Escherichia coli.
Authors: Sung, M.T. / Lai, Y.T. / Huang, C.Y. / Chou, L.Y. / Shih, H.W. / Cheng, W.C. / Wong, C.H. / Ma, C.
History
DepositionDec 9, 2011Deposition site: PDBJ / Processing site: PDBJ
SupersessionMar 14, 2012ID: 3FWM
Revision 1.0Mar 14, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Penicillin-binding protein 1B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,1632
Polymers85,5831
Non-polymers1,5811
Water3,909217
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)62.900, 289.530, 62.780
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

-
Components

#1: Protein Penicillin-binding protein 1B / PBP-1b / PBP1b / Murein polymerase / Penicillin-insensitive transglycosylase / Peptidoglycan TGase ...PBP-1b / PBP1b / Murein polymerase / Penicillin-insensitive transglycosylase / Peptidoglycan TGase / Peptidoglycan glycosyltransferase / Penicillin-sensitive transpeptidase / DD-transpeptidase


Mass: 85582.914 Da / Num. of mol.: 1 / Fragment: UNP residues 58-804
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 / Gene: b0149, JW0145, mrcB, pbpF, ponB / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P02919, peptidoglycan glycosyltransferase, Hydrolases; Acting on peptide bonds (peptidases)
#2: Chemical ChemComp-M0E / MOENOMYCIN / MOENOMYCIN / Moenomycin family antibiotics


Mass: 1580.567 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C69H106N5O34P / Comment: antibiotic*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 217 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.34 Å3/Da / Density % sol: 63.23 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 20mM Tris, 300mM NaCl, 0.28mM n-Dodecyl-N,N-dimethylamine-N-oxide (LDAO), 1.2M sodium formate, 3% 6-Aminohexanoic acid, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 1 Å
DetectorType: Bruker DIP-6040 / Detector: CCD / Date: Jul 28, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.16→30 Å / Num. all: 62891 / Num. obs: 60816 / % possible obs: 96.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.5 % / Rmerge(I) obs: 0.077
Reflection shellResolution: 2.16→2.24 Å / Redundancy: 4 % / Rmerge(I) obs: 0.497 / Mean I/σ(I) obs: 2.1 / Num. unique all: 5297 / % possible all: 85.8

-
Processing

Software
NameVersionClassification
HKL-2000data collection
SOLVEphasing
PHENIX(phenix.refine: 1.5_2)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD
Starting model: 3FWL

3fwl


Resolution: 2.161→28.845 Å / SU ML: 0.26 / σ(F): 1.33 / Phase error: 26.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2502 3072 5.06 %Random
Rwork0.2119 ---
obs0.2138 59458 97.05 %-
all-62567 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.861 Å2 / ksol: 0.327 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--7.3068 Å20 Å2-0 Å2
2--18.8366 Å20 Å2
3----11.5298 Å2
Refinement stepCycle: LAST / Resolution: 2.161→28.845 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5561 0 77 217 5855
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0055753
X-RAY DIFFRACTIONf_angle_d0.9167816
X-RAY DIFFRACTIONf_dihedral_angle_d21.0892233
X-RAY DIFFRACTIONf_chiral_restr0.064886
X-RAY DIFFRACTIONf_plane_restr0.0051012
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 22

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.1613-2.19510.40911240.3629201678
2.1951-2.2310.33991450.28212663100
2.231-2.26950.31751340.26082646100
2.2695-2.31070.29611740.25242638100
2.3107-2.35520.29811350.2322652100
2.3552-2.40320.23591380.22972690100
2.4032-2.45540.25821320.22942644100
2.4554-2.51250.24461490.22522703100
2.5125-2.57530.28521580.21192601100
2.5753-2.64490.24491380.20392690100
2.6449-2.72270.24871290.20672722100
2.7227-2.81050.22961080.20512684100
2.8105-2.91090.23661470.20842651100
2.9109-3.02730.24311610.20442689100
3.0273-3.16490.25911240.21492726100
3.1649-3.33150.25961630.21552686100
3.3315-3.53990.23151480.2085267399
3.5399-3.81270.24841340.1965262297
3.8127-4.19530.23181160.1831260393
4.1953-4.80.20711290.1761241288
4.8-6.03830.22291550.2073258894
6.0383-28.84740.26641310.2247264789
Refinement TLS params.Method: refined / Origin x: 44.5311 Å / Origin y: 97.515 Å / Origin z: -8.0359 Å
111213212223313233
T0.2435 Å2-0.025 Å2-0.0723 Å2-0.2692 Å20.0161 Å2--0.2077 Å2
L0.5651 °2-0.1946 °2-0.1712 °2-0.9359 °20.2445 °2--1.0933 °2
S-0.0787 Å °-0.0203 Å °0.1487 Å °0.0868 Å °0.0533 Å °-0.1194 Å °-0.313 Å °0.1478 Å °0.0357 Å °
Refinement TLS groupSelection details: ALL

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more